Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009516.1 Corchorus capsularis cultivar CVL-1 contig09537, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 90841
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10471 original size:11 final size:11
Alignment explanation
Indices: 10455--10479 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10445 TAGAGAACCT
10455 ATTAATGCTTA
1 ATTAATGCTTA
10466 ATTAATGCTTA
1 ATTAATGCTTA
10477 ATT
1 ATT
10480 TGGGGATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTAATGCTTA
Found at i:17033 original size:5 final size:5
Alignment explanation
Indices: 17023--17067 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
17013 TTACTTTGAT
17023 TATAA TATAA TATAA TATAA TATAA TAT-A TATATA TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA-A TATA
17068 TTCTAAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.11
5 23 0.61
6 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:17054 original size:2 final size:2
Alignment explanation
Indices: 17023--17068 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
17013 TTACTTTGAT
17023 TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17060 TA TA TA TA T
1 TA TA TA TA T
17069 TCTAAATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.13
2 34 0.87
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:40250 original size:29 final size:30
Alignment explanation
Indices: 40201--40266 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
40191 TCAAAATGCT
*
40201 CAAATAA-GAGCCTGATTTTTTAATTTGGC
1 CAAATAAGGAGCCTGATCTTTTAATTTGGC
* *
40230 CAAATAAGGGGCC-GATCTTTTAATTTGGT
1 CAAATAAGGAGCCTGATCTTTTAATTTGGC
40259 CAAATAAG
1 CAAATAAG
40267 TGCCTCATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (30 bp):
CAAATAAGGAGCCTGATCTTTTAATTTGGC
Found at i:40479 original size:59 final size:60
Alignment explanation
Indices: 40340--40486 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 60
40330 AAACTGACGC
* * * * *
40340 CAGACCCTTATTTGAACATTTTCGA-TAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGACTCTTATCTGAACATTTT-GACAAATGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
* * * *
40400 CGGGCTCTTATTTGAACATTTTGACAAATGTTAGG-CCTTATTTGGCTAAATTAAAAAAT
1 CAGACTCTTATCTGAACATTTTGACAAATGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
40459 CAGACAT-TTATCT-AAGCATTTTGACAAA
1 CAGAC-TCTTATCTGAA-CATTTTGACAAA
40487 CGCTAGATCC
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.03
59 44 0.59
60 28 0.38
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (60 bp):
CAGACTCTTATCTGAACATTTTGACAAATGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
Found at i:42315 original size:24 final size:23
Alignment explanation
Indices: 42284--42342 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
42274 TTGCTAAAAG
*
42284 GGAGAAAGAGAAGGAGAAACG-AA
1 GGAGAAAGAGAAAGAG-AACGAAA
42307 GAGAGAAAGAGAAAGAGAACGAAA
1 G-GAGAAAGAGAAAGAGAACGAAA
42331 GGAGAAGAGAGA
1 GGAGAA-AGAGA
42343 GGGTAAGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (23 bp):
GGAGAAAGAGAAAGAGAACGAAA
Found at i:52397 original size:33 final size:33
Alignment explanation
Indices: 52360--52433 Score: 78
Period size: 37 Copynumber: 2.1 Consensus size: 33
52350 TAACTTCATA
52360 CATTC-TGCAATGACCTTGGTAGCCATAGTTATT
1 CATTCATGCAATGACC-TGGTAGCCATAGTTATT
* *
52393 CATTCTAAAATGCTATGGCCTGGTAGCCATAGTTATT
1 CATTC----ATGCAATGACCTGGTAGCCATAGTTATT
52430 CATT
1 CATT
52434 AAACATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 5 0.15
37 21 0.62
38 8 0.24
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (33 bp):
CATTCATGCAATGACCTGGTAGCCATAGTTATT
Found at i:58286 original size:51 final size:51
Alignment explanation
Indices: 58231--58331 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
58221 GCAAAAGCTT
58231 GTCAATGTCAAGATGAGGGATGTT-AATCAAATTCATTTTAATAGATTGAAG
1 GTCAATGTCAAGATGAGGGA-GTTCAATCAAATTCATTTTAATAGATTGAAG
* * * *
58282 GTCAATGTTAAGATGAGGGAGTTCATTCAAATTCGTTTTCATAGATTGAA
1 GTCAATGTCAAGATGAGGGAGTTCAATCAAATTCATTTTAATAGATTGAA
58332 AAACCTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.07
51 42 0.93
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (51 bp):
GTCAATGTCAAGATGAGGGAGTTCAATCAAATTCATTTTAATAGATTGAAG
Found at i:63846 original size:6 final size:6
Alignment explanation
Indices: 63835--63888 Score: 90
Period size: 6 Copynumber: 8.8 Consensus size: 6
63825 TTTTTTCAAA
*
63835 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
63883 TAAAAA
1 -AAAAA
63889 ACCCTTTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
6 41 0.91
7 4 0.09
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:83820 original size:13 final size:13
Alignment explanation
Indices: 83802--83826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83792 TGATGGTGTA
83802 TTTTCTCTTTCTG
1 TTTTCTCTTTCTG
83815 TTTTCTCTTTCT
1 TTTTCTCTTTCT
83827 CAGACACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTCTCTTTCTG
Found at i:83966 original size:47 final size:48
Alignment explanation
Indices: 83912--84006 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 48
83902 ATCATAGGCC
*
83912 GTGCTCATACCTAGTCACAATTTTTTGC-ATTTGAGATTAATTTCGTT
1 GTGCTCATACCTAGTCACAATTTGTTGCAATTTGAGATTAATTTCGTT
*
83959 GTGCTCATACCTAGTCGCAATTTGTTGCAATTTGAGATTAATTTCGTT
1 GTGCTCATACCTAGTCACAATTTGTTGCAATTTGAGATTAATTTCGTT
84007 ATTCAGAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 26 0.58
48 19 0.42
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (48 bp):
GTGCTCATACCTAGTCACAATTTGTTGCAATTTGAGATTAATTTCGTT
Found at i:87567 original size:27 final size:27
Alignment explanation
Indices: 87529--87601 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
87519 GAAGAAAAAA
*
87529 AATAGTGATTCCCAGGAAAAGGCCATG
1 AATACTGATTCCCAGGAAAAGGCCATG
*
87556 AATACTGATTCCCAGGCAAAGGCCATG
1 AATACTGATTCCCAGGAAAAGGCCATG
* *
87583 GATATTGATTCCCAGGAAA
1 AATACTGATTCCCAGGAAA
87602 GTGATTCGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (27 bp):
AATACTGATTCCCAGGAAAAGGCCATG
Found at i:88235 original size:75 final size:75
Alignment explanation
Indices: 88112--88262 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
88102 TTAGCGTAAT
88112 CTTACAAAGGATACAAAGGAAATGCAATCATTAGCCGTAGTTGGATGCAGATCTTTTCACCGGTT
1 CTTACAAAGGATACAAAGGAAATGCAATCATTAGCCGTAGTTGGATGCAGATCTTTTCACCGGTT
88177 TCCATCCAAC
66 TCCATCCAAC
88187 CTTACAAAGGATACAAAGGAAATGCAATCATTAGCCGTAGTTGGATGCAGATCTTTTCACCGGTT
1 CTTACAAAGGATACAAAGGAAATGCAATCATTAGCCGTAGTTGGATGCAGATCTTTTCACCGGTT
88252 TCCATCCAAC
66 TCCATCCAAC
88262 C
1 C
88263 GGTATTCAAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (75 bp):
CTTACAAAGGATACAAAGGAAATGCAATCATTAGCCGTAGTTGGATGCAGATCTTTTCACCGGTT
TCCATCCAAC
Found at i:88859 original size:20 final size:21
Alignment explanation
Indices: 88820--88859 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88810 GCGTCATTTT
88820 CAGTTGGTTTCACCAAGTTTA
1 CAGTTGGTTTCACCAAGTTTA
* *
88841 CAGTT-GTTTCTCCAGGTTT
1 CAGTTGGTTTCACCAAGTTT
88860 TGACAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (21 bp):
CAGTTGGTTTCACCAAGTTTA
Done.